Posts by Vladimir Morozov

... Hi,
Is it possible to get SRA sample attributes for a given sample or
experiment ID?
Here is the sample
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS388155.
With SRAdb package:
> dbGetQuery(sra_con,"select * from sample where sample_accession =
'SRS388155' ")
sample_ID sample_alias ...

... Martin,
You are right that disagreement beween human and mouse symblos is the
problem. But you still should get some mapping if translate symbols
into
capwords
> sum(!is.na(mget(gss[[1]]@geneIds,org.Mm.egSYMBOL2EG,ifnotfound=NA)))
[1] 0
>
sum(!is.na(mget(capwords(tolower(gss[[1]]@geneIds)),or ...

... Hi
Any suggestions how to map gene symbols to mouse EntrezId(preffered)
or
Affy.
mapping to Entez apparently is not supported by GSEABase
> mapIdentifiers(gss,EntrezIdentifier())
Error in .mapIdentifiers_isMappable(from, to) :
unable to map from 'Symbol' to 'EntrezId'
neither GeneIdentifi ...

... > Yes, but if you do, and you want to use any other annotation, you
must also build that. The annotation packages are inter-connected in
non-trivial ways (many depending on GO), so mixing and matching is not
a
simple process, which is pretty much why we don't do it more often.
Essentially I ne ...